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Plant Cell. 2015 Nov;27(11):3024-37. doi: 10.1105/tpc.15.00591. Epub 2015 Nov 11.

Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidopsis.

Author information

1
Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 Cell and Molecular Biology Graduate Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104.
2
Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104.
3
Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104 Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104.
4
Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 Cell and Molecular Biology Graduate Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104 bdgregor@sas.upenn.edu.

Abstract

Posttranscriptional chemical modification of RNA bases is a widespread and physiologically relevant regulator of RNA maturation, stability, and function. While modifications are best characterized in short, noncoding RNAs such as tRNAs, growing evidence indicates that mRNAs and long noncoding RNAs (lncRNAs) are likewise modified. Here, we apply our high-throughput annotation of modified ribonucleotides (HAMR) pipeline to identify and classify modifications that affect Watson-Crick base pairing at three different levels of the Arabidopsis thaliana transcriptome (polyadenylated, small, and degrading RNAs). We find this type of modifications primarily within uncapped, degrading mRNAs and lncRNAs, suggesting they are the cause or consequence of RNA turnover. Additionally, modifications within stable mRNAs tend to occur in alternatively spliced introns, suggesting they regulate splicing. Furthermore, these modifications target mRNAs with coherent functions, including stress responses. Thus, our comprehensive analysis across multiple RNA classes yields insights into the functions of covalent RNA modifications in plant transcriptomes.

PMID:
26561561
PMCID:
PMC4682304
DOI:
10.1105/tpc.15.00591
[Indexed for MEDLINE]
Free PMC Article

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